gene_lookup: Looks up specific gene and closest peaks

In Bohdan-Khomtchouk/geneXtendeR_keepme: Optimized Functional Annotation Of ChIP-seq Data

Description

Looks up closest peak to a specified gene on the peaks file (which has been preprocessed with the peaksInput() command) based on the latest .bed file accessed or for a specified extension. This command requires a preprocessed "peaks.txt" file (generated using peaksInput()) to be present in the user's working directory, otherwise the user is prompted to rerun the peaksInput() command in order to regenerate it.

Usage

gene_lookup(organism, gene_name, n = 2, extension = NA, cutoff = Inf)

Arguments

organism	Object name assigned from readGFF() command.
gene_name	Gene names or gene ids specified by user in a string form.
n	Number of closest peaks located to 'gene_name' on any given chromosome to be found. Default = 2
extension	Desired upstream extension. If left unspecified, the latest geneXtender bed file will be chosen. If no extension is specified and no bed file can be found, a default extension of 500 is selected.
cutoff	Optional arg to specify max bp distance to search around 'gene_name'. Default = Inf

Value

A data.table with all peaks located within 'n' peaks and 'cutoff' bp distance away on every chromosome that contains 'gene_name'.

Examples

library(rtracklayer)
rat <- readGFF("ftp://ftp.ensembl.org/pub/release-84/gtf/rattus_norvegicus/Rattus_norvegicus.Rnor_6.0.84.gtf.gz")
fpath <- system.file("extdata", "somepeaksfile.txt", package="geneXtendeR")
closest <- gene_lookup(rat, c("Vom2r3", "Vom2r5"), n = 7, extension = 1000)
closest

Bohdan-Khomtchouk/geneXtendeR_keepme documentation built on June 3, 2019, 10:09 p.m.